New publication: The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes

By Martin Malmstrøm*, Ralf Britz, Michael Matschiner*, Ole K. Tørresen*, Renny Kurnia Hadiaty, Norsham Yaakob, Heok Hui Tan, Kjetill S. Jakobsen*, Walter Salzburger*, Lukas Rüber, and  Author Notes in Genome Biology and Evolution

Abstract

The world’s smallest fishes belong to the genus Paedocypris. These miniature fishes are endemic to an extreme habitat: the peat swamp forests in Southeast Asia, characterized by highly acidic blackwater. This threatened habitat is home to a large array of fishes, including a number of miniaturized but also developmentally truncated species. Especially the genus Paedocypris is characterized by profound, organism-wide developmental truncation, resulting in sexually mature individuals of <8 mm in length with a larval phenotype. Here, we report on evolutionary simplification in the genomes of two species of the dwarf minnow genus Paedocypris using whole-genome sequencing. The two species feature unprecedented Hox gene loss and genome reduction in association with their massive developmental truncation. We also show how other genes involved in the development of musculature, nervous system, and skeleton have been lost in Paedocypris, mirroring its highly progenetic phenotype. Further, our analyses suggest two mechanisms responsible for the genome streamlining in Paedocypris in relation to other Cypriniformes: severe intron shortening and reduced repeat content. As the first report on the genomic sequence of a vertebrate species with organism-wide developmental truncation, the results of our work enhance our understanding of genome evolution and how genotypes are translated to phenotypes. In addition, as a naturally simplified system closely related to zebrafish, Paedocypris provides novel insights into vertebrate development.


Published: 15 March 2018
DOI: 10.1093/gbe/evy058
Publication webpage.

* Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.
See the publication webpage for full author information

Tags: Genome Biology and Evolution;
Published May 23, 2018 10:28 AM - Last modified Nov. 8, 2018 12:16 PM